Bottom Line:
Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace.All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count.Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

Affiliation: School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK. dlarkin@rvc.ac.uk.

ABSTRACT

Background: The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed.

Results: Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n=80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes.

Conclusions: Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

Fig4: Total number of chromosomal inversions in six extant species as they diverged from the ancestor. The inversions most parsimoniously explain the patterns seen in these species. (A) For chromosomes 1–5, sufficient coverage of the lizard outgroup allowed conclusions to be drawn from an avian ancestor. (B) For chromosomes 6–28 + Z, ostrich was used as an outgroup due to the lack of coverage in the lizard. Greatest rates of change were seen in zebra finch and budgerigar. The phylogenetic tree is based on [35].

Mentions:
Overall, analysis suggests that, of the six species, the chicken lineage underwent the least number of intrachromosomal rearrangements (i.e. chicken was most similar to the common avian ancestor, probably a bipedal feathered dinosaur). Of the 46 rearrangements observed in the turkey lineage since the divergence from chicken 30 MYA (million years ago), 19 were on chromosome 1 (we believe that this may be a slight overestimate due to assembly errors in the turkey genome). The analysis also suggests that ostrich lineage underwent 44 intrachromosomal changes on chromosomes 1–5 since the divergence from the common avian ancestor (approximately 100 MYA), and the duck 28 changes since the galliform-anseriform divergence (~65 MYA). A faster rate of change was seen in the zebra finch and the budgerigar lineages, 41 in the former and 39 in the latter, occurring since the passeriform-psittaciform divergence (~54 MYA, Figure 4A). For the orthologs of chromosomes 6–28 + Z, in the absence of meaningful data from the lizard outgroup (i.e. there was minimal comparative data available), our analysis focused on the Neognathae alone (using ostrich as an outgroup, Figure 4B). Again the chicken lineage appeared to have the least number of changes compared to the ancestor and the greatest rate of change was seen in the zebra finch since the passeriform-psittaciform divergence 54 MYA (68 for zebra finch and 79 for budgerigar). For all chromosomes, the intrachromosomal events are most parsimoniously explained by a series of inversions, and the interchromosomal rearrangements by a series of translocations. We next tested the robustness of our analysis in a series of additional MGRA simulations and iterations, excluding one species at a time from the set of six species (see Methods). We were interested to know if this would affect the general chicken-like pattern of the reconstructed avian ancestor. Results showed that, although the number of reconstructed contiguous ancestral regions (CARs) tended to decrease slightly if more fragmented (scaffold-based) genome assemblies (i.e. those of budgerigar and ostrich) were excluded, near identical order of msHSBs were observed within each CAR regardless of excluding one species. The number of changes and their timescales (hence rates of change) are presented in Figure 4A (for all avian chromosomes 1–5) and 4B for the Neognathae (chromosomes 6–28 + Z).Figure 3

Fig4: Total number of chromosomal inversions in six extant species as they diverged from the ancestor. The inversions most parsimoniously explain the patterns seen in these species. (A) For chromosomes 1–5, sufficient coverage of the lizard outgroup allowed conclusions to be drawn from an avian ancestor. (B) For chromosomes 6–28 + Z, ostrich was used as an outgroup due to the lack of coverage in the lizard. Greatest rates of change were seen in zebra finch and budgerigar. The phylogenetic tree is based on [35].

Mentions:
Overall, analysis suggests that, of the six species, the chicken lineage underwent the least number of intrachromosomal rearrangements (i.e. chicken was most similar to the common avian ancestor, probably a bipedal feathered dinosaur). Of the 46 rearrangements observed in the turkey lineage since the divergence from chicken 30 MYA (million years ago), 19 were on chromosome 1 (we believe that this may be a slight overestimate due to assembly errors in the turkey genome). The analysis also suggests that ostrich lineage underwent 44 intrachromosomal changes on chromosomes 1–5 since the divergence from the common avian ancestor (approximately 100 MYA), and the duck 28 changes since the galliform-anseriform divergence (~65 MYA). A faster rate of change was seen in the zebra finch and the budgerigar lineages, 41 in the former and 39 in the latter, occurring since the passeriform-psittaciform divergence (~54 MYA, Figure 4A). For the orthologs of chromosomes 6–28 + Z, in the absence of meaningful data from the lizard outgroup (i.e. there was minimal comparative data available), our analysis focused on the Neognathae alone (using ostrich as an outgroup, Figure 4B). Again the chicken lineage appeared to have the least number of changes compared to the ancestor and the greatest rate of change was seen in the zebra finch since the passeriform-psittaciform divergence 54 MYA (68 for zebra finch and 79 for budgerigar). For all chromosomes, the intrachromosomal events are most parsimoniously explained by a series of inversions, and the interchromosomal rearrangements by a series of translocations. We next tested the robustness of our analysis in a series of additional MGRA simulations and iterations, excluding one species at a time from the set of six species (see Methods). We were interested to know if this would affect the general chicken-like pattern of the reconstructed avian ancestor. Results showed that, although the number of reconstructed contiguous ancestral regions (CARs) tended to decrease slightly if more fragmented (scaffold-based) genome assemblies (i.e. those of budgerigar and ostrich) were excluded, near identical order of msHSBs were observed within each CAR regardless of excluding one species. The number of changes and their timescales (hence rates of change) are presented in Figure 4A (for all avian chromosomes 1–5) and 4B for the Neognathae (chromosomes 6–28 + Z).Figure 3

Bottom Line:
Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace.All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count.Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

Affiliation:
School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK. dlarkin@rvc.ac.uk.

ABSTRACT

Background: The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed.

Results: Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n=80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes.

Conclusions: Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.